FMO DATABASE

FMODB ID: Y9KY2

Calculation Name: 2EJN-A-Xray547

Preferred Name:

Target Type:

Ligand Name: calcium ion

Ligand 3-letter code: CA

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2EJN

Chain ID: A

ChEMBL ID:

UniProt ID: P30438

Base Structure: X-ray

Registration Date: 2025-10-04

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Homology Modeling
Water	No
Procedure	Manual calculation
Remarks	ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	143
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1390814.777758
FMO2-HF: Nuclear repulsion	1331746.758159
FMO2-HF: Total energy	-59068.019599
FMO2-MP2: Total energy	-59232.652491

3D Structure Molmil

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:0:MET)

Summations of interaction energy for fragment #1(A:0:MET)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
-250.488	-245.763	38.189	-20.6	-22.312	-0.224

Interaction energy analysis for fragmet #1(A:0:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.704 / q_NPA : 0.844

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

Sort

Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	2	ILE	0	0.002	0.005	3.760	-4.584	-3.267	0.003	-0.646	-0.673	0.000
70	A	69	LEU	0	0.013	0.000	5.137	-7.039	-6.984	-0.001	-0.001	-0.052	0.000
71	A	70	CYS	0	-0.019	0.030	2.938	7.849	9.289	0.028	-0.505	-0.962	-0.004
72	A	71	VAL	0	0.076	0.028	1.888	-39.372	-40.052	8.285	-4.121	-3.484	-0.057
73	A	72	LYS	1	0.880	0.931	2.434	24.354	26.357	4.079	-2.653	-3.430	-0.028
74	A	73	MET	0	-0.045	0.010	2.941	10.726	11.841	0.101	-0.386	-0.831	-0.002
75	A	74	ALA	0	0.013	0.003	1.810	-34.198	-35.421	12.514	-5.829	-5.462	-0.052
76	A	75	GLU	-1	-0.865	-0.925	2.431	-51.766	-50.065	2.497	-1.375	-2.823	-0.021
77	A	76	THR	0	0.002	-0.002	1.803	-43.552	-45.001	10.677	-4.994	-4.233	-0.060
78	A	78	PRO	0	0.020	0.008	3.219	10.851	11.297	0.006	-0.090	-0.362	0.000
4	A	3	CYS	0	-0.089	-0.013	6.457	2.212	2.212	0.000	0.000	0.000	0.000
5	A	4	PRO	0	0.047	0.003	8.191	1.926	1.926	0.000	0.000	0.000	0.000
6	A	5	ALA	0	0.014	0.000	11.205	1.410	1.410	0.000	0.000	0.000	0.000
7	A	6	VAL	0	0.019	0.005	10.348	1.371	1.371	0.000	0.000	0.000	0.000
8	A	7	LYS	1	0.849	0.931	11.790	21.181	21.181	0.000	0.000	0.000	0.000
9	A	8	ARG	1	0.955	0.981	13.366	16.547	16.547	0.000	0.000	0.000	0.000
10	A	9	ASP	-1	-0.835	-0.907	15.926	-15.924	-15.924	0.000	0.000	0.000	0.000
11	A	10	VAL	0	0.016	0.003	15.313	1.032	1.032	0.000	0.000	0.000	0.000
12	A	11	ASP	-1	-0.795	-0.892	17.105	-17.883	-17.883	0.000	0.000	0.000	0.000
13	A	12	LEU	0	-0.056	-0.020	19.229	1.057	1.057	0.000	0.000	0.000	0.000
14	A	13	PHE	0	-0.013	-0.002	20.664	0.751	0.751	0.000	0.000	0.000	0.000
15	A	14	LEU	0	-0.007	0.003	19.674	0.664	0.664	0.000	0.000	0.000	0.000
16	A	15	THR	0	-0.060	-0.056	22.640	0.691	0.691	0.000	0.000	0.000	0.000
17	A	16	GLY	0	0.016	0.031	24.290	0.442	0.442	0.000	0.000	0.000	0.000
18	A	17	THR	0	-0.024	-0.049	25.883	0.231	0.231	0.000	0.000	0.000	0.000
19	A	18	PRO	0	0.020	-0.019	27.597	-0.339	-0.339	0.000	0.000	0.000	0.000
20	A	19	ASP	-1	-0.838	-0.883	28.707	-9.862	-9.862	0.000	0.000	0.000	0.000
21	A	20	GLU	-1	-0.834	-0.888	25.836	-11.608	-11.608	0.000	0.000	0.000	0.000
22	A	21	TYR	0	0.019	0.015	20.810	-0.045	-0.045	0.000	0.000	0.000	0.000
23	A	22	VAL	0	0.006	-0.002	24.015	-0.340	-0.340	0.000	0.000	0.000	0.000
24	A	23	GLU	-1	-0.940	-0.975	26.243	-10.425	-10.425	0.000	0.000	0.000	0.000
25	A	24	GLN	0	-0.079	-0.054	18.799	-0.791	-0.791	0.000	0.000	0.000	0.000
26	A	25	VAL	0	-0.004	-0.004	21.339	-0.471	-0.471	0.000	0.000	0.000	0.000
27	A	26	ALA	0	-0.026	-0.017	22.756	-0.119	-0.119	0.000	0.000	0.000	0.000
28	A	27	GLN	0	-0.077	-0.033	19.802	0.318	0.318	0.000	0.000	0.000	0.000
29	A	28	TYR	0	0.034	0.025	16.577	-0.134	-0.134	0.000	0.000	0.000	0.000
30	A	29	LYS	1	0.856	0.914	21.334	13.810	13.810	0.000	0.000	0.000	0.000
31	A	30	ALA	0	0.064	0.049	23.961	0.198	0.198	0.000	0.000	0.000	0.000
32	A	31	LEU	0	-0.050	-0.027	26.315	0.432	0.432	0.000	0.000	0.000	0.000
33	A	32	PRO	0	0.031	0.009	29.052	-0.202	-0.202	0.000	0.000	0.000	0.000
34	A	33	VAL	0	0.064	0.032	29.487	-0.151	-0.151	0.000	0.000	0.000	0.000
35	A	34	VAL	0	-0.030	-0.008	24.361	-0.190	-0.190	0.000	0.000	0.000	0.000
36	A	35	LEU	0	0.020	0.008	26.528	-0.244	-0.244	0.000	0.000	0.000	0.000
37	A	36	GLU	-1	-0.940	-0.971	28.683	-9.338	-9.338	0.000	0.000	0.000	0.000
38	A	37	ASN	0	-0.009	-0.014	27.916	0.343	0.343	0.000	0.000	0.000	0.000
39	A	38	ALA	0	0.039	0.023	25.406	-0.119	-0.119	0.000	0.000	0.000	0.000
40	A	39	ARG	1	0.850	0.902	26.732	9.880	9.880	0.000	0.000	0.000	0.000
41	A	40	ILE	0	-0.049	-0.016	29.820	0.170	0.170	0.000	0.000	0.000	0.000
42	A	41	LEU	0	0.008	0.009	23.282	0.184	0.184	0.000	0.000	0.000	0.000
43	A	42	LYS	1	0.787	0.882	25.699	12.086	12.086	0.000	0.000	0.000	0.000
44	A	43	ASN	0	0.000	-0.015	27.733	-0.034	-0.034	0.000	0.000	0.000	0.000
45	A	44	CYS	0	-0.070	0.001	26.493	0.706	0.706	0.000	0.000	0.000	0.000
46	A	45	VAL	0	0.042	0.006	24.728	0.135	0.135	0.000	0.000	0.000	0.000
47	A	46	ASP	-1	-0.831	-0.901	28.022	-11.310	-11.310	0.000	0.000	0.000	0.000
48	A	47	ALA	0	-0.061	-0.018	30.275	0.274	0.274	0.000	0.000	0.000	0.000
49	A	48	LYS	1	0.762	0.885	29.363	10.764	10.764	0.000	0.000	0.000	0.000
50	A	49	MET	0	-0.097	-0.044	23.277	-0.154	-0.154	0.000	0.000	0.000	0.000
51	A	50	THR	0	-0.004	-0.024	29.012	0.168	0.168	0.000	0.000	0.000	0.000
52	A	51	GLU	-1	-0.866	-0.961	28.462	-11.349	-11.349	0.000	0.000	0.000	0.000
53	A	52	GLU	-1	-0.863	-0.915	27.273	-11.325	-11.325	0.000	0.000	0.000	0.000
54	A	53	ASP	-1	-0.807	-0.869	26.077	-11.524	-11.524	0.000	0.000	0.000	0.000
55	A	54	LYS	1	0.850	0.915	23.906	10.957	10.957	0.000	0.000	0.000	0.000
56	A	55	GLU	-1	-0.956	-0.965	22.596	-12.709	-12.709	0.000	0.000	0.000	0.000
57	A	56	ASN	0	-0.027	-0.033	21.813	-0.919	-0.919	0.000	0.000	0.000	0.000
58	A	57	ALA	0	0.001	-0.008	20.043	-0.823	-0.823	0.000	0.000	0.000	0.000
59	A	58	LEU	0	-0.007	0.001	18.160	-1.228	-1.228	0.000	0.000	0.000	0.000
60	A	59	SER	0	0.003	-0.018	16.994	-0.973	-0.973	0.000	0.000	0.000	0.000
61	A	60	LEU	0	-0.037	-0.018	15.145	-1.126	-1.126	0.000	0.000	0.000	0.000
62	A	61	LEU	0	0.009	-0.005	13.772	-1.834	-1.834	0.000	0.000	0.000	0.000
63	A	62	ASP	-1	-0.853	-0.929	12.279	-22.851	-22.851	0.000	0.000	0.000	0.000
64	A	63	LYS	1	0.752	0.872	11.968	15.040	15.040	0.000	0.000	0.000	0.000
65	A	64	ILE	0	-0.051	-0.018	9.501	-2.299	-2.299	0.000	0.000	0.000	0.000
66	A	65	TYR	0	0.008	-0.029	7.930	-4.062	-4.062	0.000	0.000	0.000	0.000
67	A	66	THR	0	-0.033	-0.032	7.433	-3.667	-3.667	0.000	0.000	0.000	0.000
68	A	67	SER	0	0.019	0.030	8.214	-1.189	-1.189	0.000	0.000	0.000	0.000
69	A	68	PRO	0	-0.015	-0.028	6.181	-6.537	-6.537	0.000	0.000	0.000	0.000
79	A	79	ILE	0	-0.004	-0.006	6.435	5.235	5.235	0.000	0.000	0.000	0.000
80	A	80	PHE	0	0.064	0.015	8.061	3.577	3.577	0.000	0.000	0.000	0.000
81	A	81	TYR	0	-0.028	-0.022	7.157	2.918	2.918	0.000	0.000	0.000	0.000
82	A	82	ASP	-1	-0.939	-0.957	10.749	-24.212	-24.212	0.000	0.000	0.000	0.000
83	A	83	VAL	0	-0.016	-0.016	12.654	2.235	2.235	0.000	0.000	0.000	0.000
84	A	84	PHE	0	0.030	0.019	13.610	1.622	1.622	0.000	0.000	0.000	0.000
85	A	85	PHE	0	0.014	-0.005	13.206	1.520	1.520	0.000	0.000	0.000	0.000
86	A	86	ALA	0	0.001	0.008	16.546	1.256	1.256	0.000	0.000	0.000	0.000
87	A	87	VAL	0	-0.019	-0.003	18.187	1.141	1.141	0.000	0.000	0.000	0.000
88	A	88	ALA	0	0.032	0.009	19.205	0.900	0.900	0.000	0.000	0.000	0.000
89	A	89	ASN	0	-0.098	-0.060	19.464	1.214	1.214	0.000	0.000	0.000	0.000
90	A	90	GLY	0	0.023	0.009	22.547	0.424	0.424	0.000	0.000	0.000	0.000
91	A	91	ASN	0	-0.027	-0.004	20.998	0.683	0.683	0.000	0.000	0.000	0.000
92	A	92	GLU	-1	-0.777	-0.887	21.628	-12.585	-12.585	0.000	0.000	0.000	0.000
93	A	93	LEU	0	-0.008	0.002	22.755	-0.341	-0.341	0.000	0.000	0.000	0.000
94	A	94	LEU	0	-0.012	-0.018	16.339	-0.275	-0.275	0.000	0.000	0.000	0.000
95	A	95	LEU	0	0.040	0.038	17.842	-1.280	-1.280	0.000	0.000	0.000	0.000
96	A	96	ASP	-1	-0.719	-0.839	18.458	-14.239	-14.239	0.000	0.000	0.000	0.000
97	A	97	LEU	0	-0.050	-0.013	18.349	-0.283	-0.283	0.000	0.000	0.000	0.000
98	A	98	SER	0	-0.040	-0.040	13.962	-1.028	-1.028	0.000	0.000	0.000	0.000
99	A	99	LEU	0	0.051	0.019	14.447	-1.256	-1.256	0.000	0.000	0.000	0.000
100	A	100	THR	0	-0.025	-0.025	16.812	0.175	0.175	0.000	0.000	0.000	0.000
101	A	101	LYS	1	0.864	0.941	12.579	22.762	22.762	0.000	0.000	0.000	0.000
102	A	102	VAL	0	-0.036	-0.010	11.127	-1.717	-1.717	0.000	0.000	0.000	0.000
103	A	103	ASN	0	-0.039	-0.014	13.746	0.919	0.919	0.000	0.000	0.000	0.000
104	A	104	ALA	0	0.017	0.026	17.363	0.316	0.316	0.000	0.000	0.000	0.000
105	A	105	THR	0	-0.035	-0.039	18.979	0.820	0.820	0.000	0.000	0.000	0.000
106	A	106	GLU	-1	-0.814	-0.921	22.600	-12.711	-12.711	0.000	0.000	0.000	0.000
107	A	107	PRO	0	0.031	0.027	25.258	0.007	0.007	0.000	0.000	0.000	0.000
108	A	108	GLU	-1	-0.713	-0.786	19.409	-16.133	-16.133	0.000	0.000	0.000	0.000
109	A	109	ARG	1	0.737	0.855	21.101	13.757	13.757	0.000	0.000	0.000	0.000
110	A	110	THR	0	-0.021	-0.024	22.568	0.146	0.146	0.000	0.000	0.000	0.000
111	A	111	ALA	0	0.005	0.011	22.711	0.189	0.189	0.000	0.000	0.000	0.000
112	A	112	MET	0	0.003	-0.003	17.043	-0.031	-0.031	0.000	0.000	0.000	0.000
113	A	113	LYS	1	0.784	0.870	21.538	12.560	12.560	0.000	0.000	0.000	0.000
114	A	114	LYS	1	0.831	0.916	24.435	11.040	11.040	0.000	0.000	0.000	0.000
115	A	115	ILE	0	0.024	0.012	20.784	0.233	0.233	0.000	0.000	0.000	0.000
116	A	116	GLN	0	-0.044	-0.031	21.915	0.420	0.420	0.000	0.000	0.000	0.000
117	A	117	ASP	-1	-0.818	-0.912	24.021	-11.000	-11.000	0.000	0.000	0.000	0.000
118	A	119	TYR	0	0.003	-0.019	21.275	0.169	0.169	0.000	0.000	0.000	0.000
119	A	120	VAL	0	-0.023	-0.013	26.648	0.318	0.318	0.000	0.000	0.000	0.000
120	A	121	GLU	-1	-0.890	-0.944	29.146	-9.774	-9.774	0.000	0.000	0.000	0.000
121	A	122	ASN	0	-0.068	-0.044	30.057	0.637	0.637	0.000	0.000	0.000	0.000
122	A	123	GLY	0	-0.026	-0.012	31.462	0.139	0.139	0.000	0.000	0.000	0.000
123	A	124	LEU	0	-0.048	-0.041	27.114	0.115	0.115	0.000	0.000	0.000	0.000
124	A	125	ILE	0	0.009	0.016	25.443	-0.265	-0.265	0.000	0.000	0.000	0.000
125	A	126	SER	0	-0.036	-0.009	26.184	-0.227	-0.227	0.000	0.000	0.000	0.000
126	A	127	ARG	1	0.849	0.931	27.434	10.557	10.557	0.000	0.000	0.000	0.000
127	A	128	VAL	0	-0.014	-0.004	25.427	-0.500	-0.500	0.000	0.000	0.000	0.000
128	A	129	LEU	0	0.066	0.024	23.254	0.381	0.381	0.000	0.000	0.000	0.000
129	A	130	ASP	-1	-0.766	-0.864	19.040	-15.482	-15.482	0.000	0.000	0.000	0.000
130	A	131	GLY	0	0.005	0.017	18.463	-0.935	-0.935	0.000	0.000	0.000	0.000
131	A	132	LEU	0	-0.035	-0.014	18.641	-0.547	-0.547	0.000	0.000	0.000	0.000
132	A	133	VAL	0	0.026	0.022	18.817	-0.458	-0.458	0.000	0.000	0.000	0.000
133	A	134	MET	0	0.063	0.051	13.659	-1.109	-1.109	0.000	0.000	0.000	0.000
134	A	135	THR	0	-0.001	-0.002	14.004	-2.001	-2.001	0.000	0.000	0.000	0.000
135	A	136	THR	0	-0.071	-0.038	14.612	-0.341	-0.341	0.000	0.000	0.000	0.000
136	A	137	ILE	0	0.016	0.017	13.343	-0.151	-0.151	0.000	0.000	0.000	0.000
137	A	138	SER	0	-0.003	-0.013	10.023	-1.357	-1.357	0.000	0.000	0.000	0.000
138	A	139	SER	0	-0.071	-0.046	10.313	-1.310	-1.310	0.000	0.000	0.000	0.000
139	A	140	SER	0	-0.022	-0.017	12.834	1.150	1.150	0.000	0.000	0.000	0.000
140	A	141	LYS	1	0.961	0.948	12.903	13.837	13.837	0.000	0.000	0.000	0.000
141	A	142	ASP	-1	-0.920	-0.950	13.428	-17.966	-17.966	0.000	0.000	0.000	0.000
142	A	144	MET	0	-0.087	-0.025	8.416	-3.643	-3.643	0.000	0.000	0.000	0.000
143	A	145	GLY	-1	-0.935	-0.952	8.378	-24.854	-24.854	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:MET)